Research workbench
Crystal structure of the HIV-1 integrase catalytic core domain
Analyse Crystal structure of the HIV-1 integrase catalytic core domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EXQ
- Type
- protein
- Length
- 292 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pol polyprotein
- UniProt
- P04585
- Ligands
- CD, SO4, CL
- Pockets
- 5 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pol polyprotein | protein | 147 | 48% helix, 20% strand | P04585 |
| B | Pol polyprotein | protein | 145 | 48% helix, 20% strand | P04585 |
Ligands and binding sites
- CD · Cadmium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.48 | 0.78 | 18 | empty |
| 2 | 85 | 0.44 | 0.80 | 20 | empty |
| 3 | 109 | 0.43 | 0.78 | 25 | empty |
| 4 | 74 | 0.37 | 0.77 | 14 | SO4 |
| 5 | 83 | 0.36 | 0.76 | 15 | SO4 |
Interfaces
1 interface between chains.
- A–B · 1632 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 1EXQ · Crystal structure of the HIV-1 integrase catalytic core domain · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P04585
- Elsewhere: RCSB PDB 1EXQ · PDBe 1EXQ · UniProt P04585
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